In view of increasing environmental awareness and biodiversity conservation, understanding the main forcing mechanism driving biogeochemical cycles in coral reefs and lagoon coastal areas is a priority. La Niña events cause unbalanced situations in the Equatorial Pacific and result in enhanced precipitation in South West Pacific coastal areas. We investigated the impact of heavy rainfalls during the 2008 La Niña event on the New Caledonia lagoon using a 3D coupled on-line hydrodynamic–biogeochemical model. Simulations and data showed that the whole lagoon was impacted by river inputs and stronger hydrodynamics, enhancing chlorophyll-a concentration by a factor between 1.7 and 1.9. The coupled model provided new insights into plume transport, highlighting that eastern plumes can be advected northwards or can reach the South West Lagoon, depending on the balance between regional, tide-induced, and wind-induced surface currents. It also provided a synoptic view of lagoon biogeochemical–hydrodynamic response, when remote sensing data are not available due to cloud coverage.

The keynote paper by Garrett Hardin 44years ago introduced the term ‘tragedy of the commons’ into our language (Hardin, 1968); this term is now used widely, but it is neither universally accepted nor fully understood. Irrespective, the ‘tragedy of the commons’ is an increasing reality for more than 500 million people that rely on the biodiversity resources and services of tropical coral reefs, mangrove forests, seagrass beds and associated fisheries. These natural resources continue to decline despite major advances in our scientific understanding of how ecosystems and human populations interact, and the application of considerable conservation and management efforts at scales from local user communities to oceans. Greater effort will be required to avert increasing damage from over-exploitation, pollution and global climate change; all deriving from increasing exploitation driven by poverty and progress i.e. continuing to expand development indefinitely and extraction of resources at industrial scales. However, the ‘tragedy’ concept has been widely criticized as a simple metaphor for a much larger set of problems and solutions. We argue that the ‘tragedy’ is essentially real and will continue to threaten the lives of millions of people unless there are some major moral and policy shifts to reverse increasing damage to coastal habitats and resources. We agree with the conclusion by Hardin that the solution to the tragedy will not be through the application of natural sciences, but via implementing exceedingly difficult and controversial moral decisions. An extreme example of a moral and controversial direction suggested by Hardin was in re-examining the ‘freedom to breed’ as an inherent human value. The need for ‘moral decisions’ is even greater in 2012.

Coastal and inshore areas of the Great Barrier Reef lagoon receive substantial amounts of material from adjacent developed catchments, which can affect the ecological integrity of coral reefs and other inshore ecosystems. A 5-year water quality monitoring dataset provides a ‘base range’ of water quality conditions for the inshore GBR lagoon and illustrates the considerable temporal and spatial variability in this system. Typical at many sites were high turbidity levels and elevated chlorophyll a and phosphorus concentrations, especially close to river mouths. Water quality variability was mainly driven by seasonal processes such as river floods and sporadic wind-driven resuspension as well as by regional differences such as land use. Extreme events, such as floods, caused large and sustained increases in water quality variables. Given the highly variable climate in the GBR region, long-term monitoring of marine water quality will be essential to detect future changes due to improved catchment management.

In July 2001, the National Museum of Marine Biology and Aquarium, co-sponsored by the Kenting National Park Headquarters and Taiwan’s National Science Council, launched a Long-Term Ecological Research (LTER) program to monitor anthropogenic impacts on the ecosystems of southern Taiwan, specifically the coral reefs of Kenting National Park (KNP), which are facing an increasing amount of anthropogenic pressure. We found that the seawater of the reef flats along Nanwan Bay, Taiwan’s southernmost embayment, was polluted by sewage discharge at certain monitoring stations. Furthermore, the consequently higher nutrient and suspended sediment levels had led to algal blooms and sediment smothering of shallow water corals at some sampling sites. Finally, our results show that, in addition to this influx of anthropogenically-derived sewage, increasing tourist numbers are correlated with decreasing shallow water coral cover, highlighting the urgency of a more proactive management plan for KNP’s coral reefs.

This study examined the distribution of virioplankton and bacterioplankton in two coral reef systems (Ahe and Takaroa atolls) in the Tuamotu Archipelago, in comparison with the surrounding oligotrophic ocean. Mean concentrations of 4.8×10⁵ and 6.2×10⁵cellsml⁻¹ for bacteria and 8.1×10⁶ and 4.3×10⁶VLP(virus-like particle) ml⁻¹ were recorded in Ahe and Takaroa lagoons, respectively. Chlorophyll-a concentrations and dissolved organic matter were higher in Ahe whereas ³H thymidine incorporation rates were higher in Takaroa. First data on lytic and lysogenic strategies of phages in coral reef environments were discussed in this paper. The fraction of visibly infected cells by viruses was negligible regardless of the lagoon station (mean=0.15%). However, the fraction of lysogenic cells ranged between 2.5% and 88.9%. Our results suggest that the distribution patterns of virioplankton are apparently not coupled to the spatial dynamics of the bacterioplankton communities.

In north Western Australia coral reefs occur near ports being developed to support rapidly expanding resources industries. Dredging for port construction is required to stop during significant mass coral spawning events due to the sensitivity of gametes and larvae to increases in turbidity and sedimentation, but the timing of this event can vary between seasons and years so monitoring is used to predict when spawning is imminent. Here we used simulations to mimick sampling strategies currently used in some coral spawning monitoring programmes in Western Australia, to assess the ability of these programmes to be able to predict multi-specific mass spawning events. We found that current practices may sometimes miss spawning events that are likely to be considered large enough to warrant stopping dredging. Generally, sampling fewer individuals in a large number of species is a better way of monitoring for upcoming spawning than sampling a large number of individuals in a small number of species, but overall, greater sampling efforts than are currently undertaken are needed if moderately sized events are to be detected reliably. Determining exactly how many samples are needed, however, depends on having a clearer definition of what actually constitutes a “significant mass spawning” event in the first place.

The coral reef at Kahekili, Maui is located ∼300m south of the Lahaina Wastewater Reclamation Facility which uses four Class V injection wells to dispose of 3–5million gallons of wastewater effluent daily. Prior research documented that the wastewater effluent percolates into the nearshore region of Kahekili. To determine if the wastewater effluent was detectable in the surface waters offshore, we used algal bioassays from the nearshore region to 100m offshore and throughout the water column from the surface to the benthos. These algal bioassays documented that significantly more wastewater effluent was detected in the surface rather than the benthic waters and allowed us to generate a three-dimensional model of the wastewater plume in the Kahekili coastal region. Samples located over freshwater seeps had the highest δ¹⁵N values (∼30–35‰) and the effluent was detected in surface samples 500m south and 100m offshore of the freshwater seeps (∼8–11‰).

Understanding the linkages between coastal watersheds and adjacent coral reefs is expected to lead to better coral reef conservation strategies. Our study aims to examine the main predictors of environmental proxies recorded in near shore corals and therefore how linked near shore reefs are to the catchment physical processes. To achieve these, we developed models to simulate hydrology of two watersheds in Madagascar. We examined relationships between environmental proxies derived from massive Porites spp. coral cores (spectral luminescence and barium/calcium ratios), and corresponding time-series (1950–2006) data of hydrology, climate, land use and human population growth. Results suggest regional differences in the main environmental drivers of reef sedimentation: on annual time-scales, precipitation, river flow and sediment load explained the variability in coral proxies of river discharge for the northeast region, while El Niño-Southern Oscillation (ENSO) and temperature (air and sea surface) were the best predictors in the southwest region.

The effects of the photosystem II (PSII) herbicide diuron was assessed on thirteen tropical foraminifera hosting diatom, dinoflagellate, red or green algae endosymbionts. Inhibition of photosynthesis (reduced ΔF/Fₘ ′) by diuron depended on both symbiont type and test ultrastructure, with greatest sensitivity observed for diatom- and chlorophyte-hosting species (24h IC₂₅ 2.5–4μgL⁻¹). Inhibition kinetics was slow (24–48h until maximum inhibition) in comparison with corals, suggesting structural differences may influence herbicide uptake and transport. Although foraminifera were generally less sensitive to direct effects of diuron (inhibition ΔF/Fₘ ′) than other marine phototrophs, damage to PSII (reduction Fᵥ/Fₘ) occurred at concentrations lower than observed for other organisms (24h IC₂₅ 3–12μgL⁻¹). Damage to PSII was highly light dependent and occurred at very low light intensities indicating limited photoprotective capacity. The high diversity, widespread occurrence and relative sensitivity make foraminifera good bioindicator organisms to evaluate phytotoxic stress on coral reefs.

We propose a framework for spatially estimating a proxy for coral reef resilience using remote sensing. Data spanning large areas of coral reef habitat were obtained using the commercial QuickBird satellite, and freely available imagery (NASA, Google Earth). Principles of coral reef ecology, field observation, and remote observations, were combined to devise mapped indices. These capture important and accessible components of coral reef resilience. Indices are divided between factors known to stress corals, and factors incorporating properties of the reef landscape that resist stress or promote coral growth. The first-basis for a remote sensed resilience index (RSRI), an estimate of expected reef resilience, is proposed. Developed for the Red Sea, the framework of our analysis is flexible and with minimal adaptation, could be extended to other reef regions. We aim to stimulate discussion as to use of remote sensing to do more than simply deliver habitat maps of coral reefs.